From chemistry-request@ccl.net Wed Jan 26 22:39:54 2005 Received: from web30804.mail.mud.yahoo.com (web30804.mail.mud.yahoo.com [68.142.200.147]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0R3dp7a012524 for ; Wed, 26 Jan 2005 22:39:51 -0500 Received: (qmail 66813 invoked by uid 60001); 27 Jan 2005 03:39:51 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=naTq/iDEuknqHCMY6rZsI7KsysQeR9DyCuby+UUXI3gco7QMCY1BEwWYLezCYAYb7aEAuh4DZ0EMykam8JZ5E3V+Agdc4ayGFeBKQviK1PaapQqMFKB4MX7nK7ntpKPnoJtl0WUeAEMfKUdkjBrCKwg+uPf2n0UtWWrNfcFnDg8= ; Message-ID: <20050127033951.66811.qmail.-at-.web30804.mail.mud.yahoo.com> Received: from [68.46.0.3] by web30804.mail.mud.yahoo.com via HTTP; Wed, 26 Jan 2005 19:39:50 PST Date: Wed, 26 Jan 2005 19:39:50 -0800 (PST) From: Guosheng Wu Subject: Re: CCL:orbitals and reality To: chemistry.-at-.ccl.net In-Reply-To: <20050123083429.79099.qmail.-at-.web51303.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=6.1 required=7.5 tests=FORGED_YAHOO_RCVD, FROM_ENDS_IN_NUMS,FROM_HAS_ULINE_NUMS,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net One of the by-products on this topic is that one might get a chance to know some new scientific journal names somewhere in the messages... good or bad, the readers will know... I do not read many journals, but at least 2 papers below on theoretical chemistry seem to be much more worth reading and also entertaining than some messages in CCL: 1. "A Conversation on VB vs MO Theory: A Never-Ending Rivalry?" R. Hoffmann, S. Shaik & P.C. Hiberty, Acc. Chem. Res. 2003,36,750. (Do not forget to check the cover of that issue: holywood style post) 2.1 "Comment on Molecular Mechanics for Chemical Reactions," J. Florian, J. Phys. Chem. A 106, 5046-5047 (2002). 2.2 "Reply to Comment on Molecular Mechanics for Chemical Reactions," D. G. Truhlar, Journal of Physical Chemistry A 106, 5048-5051 (2002). Regards, -Guosheng Wu __________________________________ Do you Yahoo!? Take Yahoo! Mail with you! Get it on your mobile phone. http://mobile.yahoo.com/maildemo From chemistry-request@ccl.net Thu Jan 27 09:22:58 2005 Received: from impact.dyn.unipg.it (impact.dyn.unipg.it [141.250.17.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0REMvUI001959 for ; Thu, 27 Jan 2005 09:22:57 -0500 Received: from impact.dyn.unipg.it (localhost [127.0.0.1]) by impact.dyn.unipg.it (8.12.10+Sun/8.12.10) with ESMTP id j0REMtDs010706 for ; Thu, 27 Jan 2005 15:22:55 +0100 (CET) Received: from localhost (max@localhost) by impact.dyn.unipg.it (8.12.10+Sun/8.12.10/Submit) with ESMTP id j0REMt9I010703 for ; Thu, 27 Jan 2005 15:22:55 +0100 (CET) Date: Thu, 27 Jan 2005 15:22:55 +0100 (CET) From: Porrini Massimiliano To: chemistry -()- ccl.net Subject: Re: CCL:Coupling Constants in Barostats and/or Thermostats In-Reply-To: <7A315585-6E27-11D9-AF18-000393AEC93C -()- few.vu.nl> Message-ID: References: <7A315585-6E27-11D9-AF18-000393AEC93C -()- few.vu.nl> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi * I want to thank the precious hints of Marcel Swart and David A. Case. I've read the papers prompted by them and I've found interesting concepts which can help me. Best Regards Massimiliano Porrini PS: I would to thank also the community of CCL for its existence and because she allows us to have use of this helpful service. +++++++++++++++++++++++++++++++++++++++++++++++++ Dott. Massimiliano Porrini Dipartimento di Chimica Universita` degli Studi di Perugia Via Elce di Sotto, 8 06123 Perugia (PG) Italia Tel. +39 075 585 5527 Fax +39 075 585 5606 e-mail max -()- dyn.unipg.it +++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@ccl.net Thu Jan 27 13:07:15 2005 Received: from simbiosys.ca ([65.18.214.160]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0RI7DUI010378 for ; Thu, 27 Jan 2005 13:07:14 -0500 Received: from phobos.simbiosys.ca (CPE0080c6f1fcb9-CM000f9f7b41ce.cpe.net.cable.rogers.com [70.26.20.9]) (authenticated (0 bits)) by simbiosys.ca (8.12.10/8.11.0) with ESMTP id j0RGwTUB021049 for ; Thu, 27 Jan 2005 11:58:30 -0500 X-Authentication-Warning: simbiosys.ca: simbiosys owned process doing -bs From: Aniko Simon Organization: SimBioSys Inc. To: chemistry)at(ccl.net Subject: CCL: Announcing SPROUT v6.0 de novo ligand design software Date: Thu, 27 Jan 2005 11:59:03 -0500 User-Agent: KMail/1.5.3 MIME-Version: 1.0 Content-Disposition: inline Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Message-Id: <200501271159.03782.aniko)at(simbiosys.ca> X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL members, The ability to design drugs that bind strongly within a receptor site has long been a goal of medicinal/computational chemists. The latest version of the sophisticated program, SPROUT v6.0, brings chemists closer to that goal. SPROUT v6.0 is a mature de novo ligand design package that gives users unsurpassed control over the drug design process, while allowing for automated options. SPROUT v6.0 takes advantage of parallel processing environments to reach state-of-the-art computational speeds. SPROUT v6.0 has an impressive list of features: * Exhaustive and systematic coverage of the search space * Excellent visualization capabilities * Generic skeletons that represent all interesting chemical space * Improved loan pair directionality * Complexity analysis for ranking and pruning structures * Specific library for peptide generation * Plus many, many, more!! SPROUT v6.0 is highly tuned for Linux and Silicon Graphics IRIX operating systems. To receive a free evaluation version of SPROUT v6.0, please email SimBioSys at info)at(simbiosys.ca or visit our website at www.simbiosys.ca. Thanks, Best regards, Ms Aniko Simon, Ph.D. -- VP Business Development SimBioSys Inc. Toronto, Canada From chemistry-request@ccl.net Thu Jan 27 11:54:47 2005 Received: from mail.chemistry.gatech.edu (mail.chemistry.gatech.edu [130.207.36.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0RGslUI007669 for ; Thu, 27 Jan 2005 11:54:47 -0500 Received: from aurelius.chemistry.gatech.edu (aurelius.chemistry.gatech.edu [130.207.35.94]) by mail.chemistry.gatech.edu (8.12.8/8.12.8) with ESMTP id j0REvcbc018908 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for >ccl.net>; Thu, 27 Jan 2005 09:57:38 -0500 Date: Thu, 27 Jan 2005 10:09:06 -0500 (EST) From: David Sherrill >chemistry.gatech.edu> X-X-Sender: sherrill<>localhost.localdomain To: chemistry<>ccl.net Subject: Georgia Tech Summer Theory Program 2005 Message-ID: >localhost.localdomain> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Georgia Tech will host its third annual Summer Theory Program as part of its NSF-sponsored Reserach Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 23 to July 29 and is open to students who will be in their junior or senior years during the 2005-2006 academic year. Theory students will work with Professors David Sherrill or Rigoberto Hernandez in the areas of electronic structure theory or dynamics. The research experience is supplemented by an introductory lecture series in theoretical chemistry. Successful applicants will receive a stipend of $3500, a travel allowance, and on-campus dormitory housing. Further details are available at http://vergil.chemistry.gatech.edu/opp/summer.html The deadline for applications is February 15, 2005. -- C. David Sherrill, Ph.D. sherrill<>chemistry.gatech.edu Assistant Professor of Chemistry Phone: (404) 894-4037 School of Chemistry and Biochemistry Fax: (404) 894-7452 Georgia Institute of Technology http://www.chemistry.gatech.edu/faculty/sherrill/ From chemistry-request@ccl.net Thu Jan 27 14:59:00 2005 Received: from smtp1.server.rpi.edu (smtp1.server.rpi.edu [128.113.2.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0RJwuUI014286 for ; Thu, 27 Jan 2005 14:58:56 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp1.server.rpi.edu (8.13.0/8.13.0) with ESMTP id j0RIqJQp024090 for ; Thu, 27 Jan 2005 13:52:19 -0500 Message-Id: <200501271852.j0RIqJQp024090 = = = smtp1.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: chemistry = = = ccl.net From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute X-Originating-Ip: 128.113.135.209 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Thu, 27 Jan 2005 13:52:18 EST X-Mailer: EMUmail 4.00 Subject: CCL: On orbitals and "reality" X-CanItPRO-Stream: default X-RPI-SA-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=2.5 required=7.5 tests=COMBINED_FROM,IMPRONONCABLE_1, SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I have been following the discussion on "Orbitals and Reality" with considerable interest, but wanted to hold off responding until I had a chance to examine the Nature paper. "Elements of physical reality" formed a major component of the early 20th century debates between Einstein and the Copenhagen school, but I had not realized that "reality" still constitutes an element of scientific discourse today. "Reality" is not something that has a rigorous scientific definition (apart from the unfortunate confusion with the real, imaginary and complex nembers of mathematics); so I prefer not to talk about "reality" in a scientific discussion. Experimental observations constrain the objects and language of theory; theoretical concepts, in turn, frame the questions that experiments are designed to answer and interpret the experimental observations. If this loop can be closed in an internally consistent manner, that imparts a degree of experimental confirmation to the objects of theory. If not, it is time to either repeat the experiments, tinker with the theoretical concepts or design new ones. Someone mentioned unicorns. If unicorns (or dark energy or ...) help explain experimental observations, then they will constitute legitimate objects for scientific discourse and experimental design. That is all there is to it! "Reality" is for philosophers (with apologies to the philosophers here; we are scientists... why should we worry about reality? :-) A little over a hundred years ago, theories of motion were formulated in terms of the aether and experiments were designed to detect the motion of bodies relative to the aether. Today our theories are formulated in terms of spacetime and experiments are designed to detect the curvature of spacetime. Does that make spacetime "real" and the aether "unreal"? Would it have made a difference to our world if we had continued using the term "aether" with new topological, rather than material, properties? We tend to think of molecular structure as "real" -- after all, we can "see" structure maps come out of our X-ray machines. But the X-rays are only producing diffraction patterns and it is the software (guided by the concepts and equations of theory) that produces the structure maps. We often tend to think of electrons as moving around in charge clouds and nuclei as quasi-localized at any point in time, with definite internuclear (bond) distances and bond angles. But there is no fundamental reason to think this way, apart from convenience (and the thousand-fold mass difference). The nuclei too are delocalized in charge clouds with the protrons indistinguishable among themselves and the neutrons likewise. But we donot usually question whether bond lengths and bond angles are "real". Orbitals have no meaning in VB theory or in the Hohenberg-Kohn variational version of DFT (as distinguished from the Kohn-Sham version). These theories cannot help design experiments to "observe orbitals" and would interpret the observations of Villeneuve, et al, very differently. While historically, orbitals may have derived from Bohr-Sommerfeld orbits, their only significance in the quantum mechanics of many-electron systems derives > from a theorem of linear algebra which states that the eigenfunctions of a Hermitian operator (e.g. the hydrogen atom Hamiltonian) form a complete set for the expansion of any (wave) function. Since no one uses a complete set (which is infinite), we could as well use plane waves or Gaussians or wavelets for our expansions... and we do! For a computational chemist doing CI, orbitals have about as much "reality" as primitive Gaussians have for an organic chemist doing HF computations. Nevertheless I donot understand the reluctance to accept the interpretation of Villeneuve, et al's observations in terms of orbitals. It is an accepted fact that an electron undergoing ionization does not "flow" out continuously and uniformly from throughout the atom or molecule. The hole formed by ionization of the electron has a definite quantum of charge, a definite quantum of spin and a characteristic shape. Let us say Villeneuve, et al have observed the hole formed by the ionization of an electron from N2 ... would this be more acceptable? Note that they have observed not just the density hole, but by coherent recombination, the relative phase as well. So what's the problem with calling this an orbital? Unfortunately, Villeneuve, et al donot help their case by showing a diagrammatic representation of their reconstructed wavefunction alongside a N2 2p sigma_g orbital "from an ab initio calculation" but they omit to mention the basis set or level of theory employed, making any quantitative comparison moot. The concept of an orbital has different meanings in different contexts, but in its essence an orbital is a solution to a one-electron equation or an "effective" one-electron equation of motion. The replacement of the interelectronic repulsion term by an effective one-electron potential is at the heart of the Hartree-Fock and Kohn-Sham procedures that generate a system of one-electron equations. Within these theories, it is legitimate to formulate some explanations in terms of orbitals (bearing in mind the approximations involved and thus the approximate nature of the explanations) and to design experiments to test these approximations (e.g. Koopmans' theorem, Wodward-Hoffman rules). Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From chemistry-request@ccl.net Thu Jan 27 18:53:12 2005 Received: from lakermmtao07.cox.net (lakermmtao07.cox.net [68.230.240.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0RNr8UI021336 for ; Thu, 27 Jan 2005 18:53:09 -0500 Received: from [192.168.253.3] (really [68.9.51.109]) by lakermmtao02.cox.net (InterMail vM.6.01.04.00 201-2131-117-20041022) with ESMTP id <20050127223841.TKBW2202.lakermmtao02.cox.net@[192.168.253.3]> for ; Thu, 27 Jan 2005 17:38:41 -0500 User-Agent: Microsoft-Entourage/11.1.0.040913 Date: Thu, 27 Jan 2005 17:38:42 -0500 Subject: CCL: set stack size with ulimit under OS X 10.3 From: Kenneth Overly To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I'm trying to run AutoDock on a dual 2 GHz G5 running OS X 10.3. Fortunately, the folks at Scripps have provided precompiled binaries of AutoDock and AutoGrid for OS X. My problem is setting the stack size to unlimited under OS X. Like Linux, OS X uses a bashrc file for systemwide bash configuration. I can edit the file to add "ulimit -s unlimited" as superuser (using sudo) but OS X won't allow my default account (which has administrator privileges) to modify the stack size. I'm pretty sure this has something to do with the peculiarities of OS X but I'm not sure how to fix it. Can anyone shed some light? -- Kenneth R. Overly, Ph.D., Assoc. Prof. of Chemistry Providence College Dept. of Chemistry and Biochemistry Providence, RI 02918